Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg, Russian Federation.
Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China.
J Comput Aided Mol Des. 2020 Nov;34(11):1157-1169. doi: 10.1007/s10822-020-00330-0. Epub 2020 Jul 10.
Experimental 3D structures of calcium channels with phenylalkylamines (PAAs) provide basis for further analysis of atomic mechanisms of these important cardiovascular drugs. In the crystal structure of the engineered calcium channel CavAb with Br-verapamil and in the cryo-EM structure of the Cav1.1 channel with verapamil, the ligands bind in the inner pore. However, there are significant differences between these structures. In the crystal structure the ligand ammonium group is much closer to the ion in the selectivity-filter region Site 3, which is most proximal to the inner pore, than in the cryo-EM structure. Here we used Monte Carlo energy minimizations to dock PAAs in calcium channels. Our computations suggest that in the crystal structure Site 3 is occupied by a water molecule rather than by a calcium ion. Analysis of the published electron density map does not rule out this possibility. In the cryo-EM structures the ammonium group of verapamil is shifted from the calcium ion in Site 3 either along the pore axis, towards the cytoplasm or away from the axis. Our unbiased docking reproduced these binding modes. However, in the cryo-EM structures detergent and lipid molecules interact with verapamil. When we removed these molecules, the nitrile group of verapamil bound to the calcium ion in Site 3. Models of Cav1.2 with different PAAs suggest similar binding modes and direct contacts of the ligands electronegative atoms with the calcium ion in Site 3. Such interactions explain paradoxes in structure-activity relationships of PAAs.
用苯烷胺（PAA）构建的钙通道实验 3D 结构为进一步分析这些重要心血管药物的原子机制提供了基础。在带 Br-维拉帕米的工程钙通道 CavAb 的晶体结构和带维拉帕米的 Cav1.1 通道的 cryo-EM 结构中，配体在内腔结合。然而，这些结构之间存在显著差异。在晶体结构中，配体的铵基团与选择性过滤器区域 Site 3 中的离子（离内腔最近）的距离比在 cryo-EM 结构中更近。在此，我们使用蒙特卡罗能量最小化将 PAA 对接至钙通道中。我们的计算表明，在晶体结构中，Site 3 被水分子占据，而不是钙离子。对已发表的电子密度图的分析并不能排除这种可能性。在 cryo-EM 结构中，维拉帕米的铵基团沿孔轴、朝向细胞质或远离轴从 Site 3 中的钙离子上发生位移。我们的无偏对接重现了这些结合模式。然而，在 cryo-EM 结构中，去污剂和脂质分子与维拉帕米相互作用。当我们去除这些分子时，维拉帕米的腈基与 Site 3 中的钙离子结合。不同 PAA 的 Cav1.2 模型表明类似的结合模式以及配体的电负性原子与 Site 3 中的钙离子的直接接触。这些相互作用解释了 PAA 的结构-活性关系中的悖论。
